Answer
A confirmed working workaround (after escalating to IFS support without a definitive root-cause fix) was enabling 'Allow Lapses in Number Sequences' on the Coordinator Group used for these orders — found at Application Base Setup > General Data > Coordinator Groups, on the relevant Coordinator Group record. After enabling this checkbox, the false 'object already exists' errors on incoming EDI orders stopped recurring, even across later update levels where the underlying issue apparently still exists in some form. This points to the false-positive 'already exists' check being tied to how the Customer Order numbering sequence is validated, which the lapses-allowed setting relaxes.